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Reassortment events such as this can only be discovered by sequencing multiple virus segments.
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The name of an influenza virus, like H1N1, describes two of the eight virus segments.
No evidence was found for reassortment of virus segments.
SBV has been identified as most related to Sathuperi virus, and for the small and large segments, Shamonda virus segments show the highest sequence identity.
Because influenza viruses reassort, different event histories should be visible in phylogenies inferred separately for the 8 virus segments.
Samples from co-infected hosts will have RNA present from multiple viruses [31], and culture and PCR amplification may result in specific segment sub-regions being amplified from different viruses, giving the appearance of homologous intra-segment recombination where none has occurred.
Antigenic drift is the frequent occurrence of point mutations resulting from defects in RNA replication mechanisms, while antigenic shift is less frequent, involving re-assortment of the RNA segments arising from exchanges between different strains in host cells infected by multiple viruses.
Perhaps most disturbing is that one tick can transmit a "cocktail" of multiple viruses at once.
Multiple viruses were identified in 41 patients.
We observed ≈70% overall average nucleotide sequence percentage identity with Dhori virus in multiple genomic segments.
Phylogenetic analyses were conducted on deduced amino acid sequences from multiple genomic segments of selected viruses of the same viral family by using MEGA 5.05 software (http://www.megasoftware.net/) as described (16 ).
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